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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...These authors contributed equally to this review. Corresponding author: christopher.pearson@sickkids.caAbstractExpansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
...in some plant lineages (Clark et al. 2007; Xu et al. 2009).The abundance of STRs in eukaryotic promoters (Sawaya et al. 2013), and their associations with gene expression (in cis) (Vinces et al. 2009; Bilgin Sonay et al. 2015; Gymrek et al. 2015), suggested that STRs affect transcription, possibly...
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Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
- Eli Rodgers-Melnick,
- Shrinivasrao P. Mane,
- Palitha Dharmawardhana,
- Gancho T. Slavov,
- Oswald R. Crasta,
- Steven H. Strauss,
- Amy M. Brunner,
- and Stephen P. DiFazio
Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
...(ChenandNi 2006;Gaeta et al. 2006; Tate et al. 2009; Wang et al. 2010). Clusters of duplicated genes have also formed through tandem duplication (TD) processes, which have greatly expanded some gene families, such as the Nucleotide Binding Site-Leucine Rich Repeat (NBS-LRR) subset of plant resistance genes...
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Research: Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen
- Ronnie de Jonge,
- Melvin D. Bolton,
- Anja Kombrink,
- Grardy C.M. van den Berg,
- Koste A. Yadeta,
- and Bart P.H.J. Thomma
Genome Res. August 2013 23: 1271-1282; Published in Advance May 16, 2013, doi:10.1101/gr.152660.112
...results suggest that asexual pathogens may evolve by prompting chromosomal rearrangements, enabling rapid development of novel effector genes. Likely, chromosomal reshuffling can act as a general mechanism for adaptation in asexually propagating organisms. [Supplemental material is available...
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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...segments, which promote reduction and expansion of the gene repertoire, respectively (Llorente et al. 2000; Dujon et al. 2004; Wapinski et al. 2007; Butler et al. 2009; Souciet et al. 2009; Scannell et al. 2011;Gabaldonet al. 2013).Whole-duplication (WGD) and hybridization events also affect gene...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...diverse life forms, including plants, fungi, and nematodes. However, our understanding of its molecular basis, particularly in animals, remains limited. Aphelenchus avenae nematodes are notable for their exceptional tolerance to dehydration, and multiple genes related to this trait have been identified...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
..., demonstrating an unprecedented putative cis-regulatory role of Helitrons in Drosophila. Differential expression analysis between species with different preferred hosts reveals divergence in gene expression in heads and larvae. Although TEs’ presence does not affect overall gene expression, we observe 6...
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Research: RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology
- Andrew R.J. Lawson,
- Guy F.L. Hindley,
- Tim Forshew,
- Ruth G. Tatevossian,
- Gabriel A. Jamie,
- Gavin P. Kelly,
- Geoffrey A. Neale,
- Jing Ma,
- Tania A. Jones,
- David W. Ellison,
- and Denise Sheer
Genome Res. April 2011 21: 505-514; Published in Advance March 10, 2011, doi:10.1101/gr.115782.110
...were KIAA1549–BRAF exon 16–exon 11 (PA27) and SRGAP3–RAF1 exon 11–exon 8 (PA30). Our initial characterization of the SRGAP3– RAF1 fusion identified an internal tandem duplication of SRGAP3 exon 11, which enables the resultant fusion gene to be in-frame (Forshew et al. 2009). We successfully sequenced...
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Research: Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts
- Ricardo DeMarco,
- William Mathieson,
- Sophia J. Manuel,
- Gary P. Dillon,
- Rachel S. Curwen,
- Peter D. Ashton,
- Alasdair C. Ivens,
- Matthew Berriman,
- Sergio Verjovski-Almeida,
- and R. Alan Wilson
Genome Res. August 2010 20: 1112-1121; Published in Advance July 6, 2010, doi:10.1101/gr.100099.109
...(Fig. 2A). Alignment of the protein products using BLASTP indicates that the first three members have ;60% identity and 70% positive amino acids, with a fourth more divergent member (MEG-3.4; ;25% identity and 40%positive).We interpret this organization to be the result of a series of gene duplications...
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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...boundary duplications largely overlap with functional regulatory elements and genes argues for further examining the forces shaping enrichment of TDs at TAD boundaries. Collectively, our findings offer novel insight into the evolutionary significance of spatial organization in shaping patterns of large...

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